Despite letting the Phoenix back into the contest on multiple occasions, Victory made their moments count in attack and held on late to claim their first win on the road this season and climb to fifth.
"We haven't been getting good enough results on the road, so today was very important," Victory star man Juan Mata told Sky Sports NZ.
Socceroo Nishan Velupillay was a constant attacking threat and talented defender Sebastian Esposito was superb, while Wellington attacker Carlo Armiento consistently caused havoc.
"I thought that performance was one we haven't had this year - three goals but we slogged it out for 20 minutes there. Very proud of the boys," Velupillay said.
The 10th-placed Phoenix had been buoyed by the signing of former wunderkind Sarpreet Singh, on loan from Backa Topola in the Serbian SuperLiga, until season's end.
And Wellington nearly kept the good vibes going when Tim Payne forced a big save from Victory's Jack Warshawsky in the second minute.
But eight minutes later, Esposito flicked on a Reno Piscopo corner to open the scoring.
After peppering the Victory goal, Wellington equalised off the back of a rare Mata turnover in the 39th minute.
Ramy Najjarine pounced, intercepting and bursting forward before working the ball to Armiento, who rifled home.
For Victory's second, Denis Genreau worked the ball to Charles Nduka who flicked it on to Velupillay to steer Victory back in front.
Wellington received a penalty in the 64th minute when Armiento sucked Josh Rawlins into unnecessarily legging him.
There was a VAR review, seemingly checking whether contact was inside the area - then referee Jack Morgan contentiously ruled it was normal football contact, not a foul.
"It was a very like 50-50 decision, I felt," stand-in Phoenix skipper Kazuki Nagasawa told Sky Sports NZ.
"We couldn't get the penalty, it was a big opportunity for us."
Victory made it 3-1 when Velupillay slipped through Keegan Jelacic, who brilliantly cut the ball back for fellow substitute Louis D'Arrigo to meet with a bullet header from a late run into the six-yard box.
Wellington hit back when a wicked Armiento corner deflected off Roderick Miranda for an own goal in the 84th minute.
Victory held on through nine minutes of chaotic injury time, including D'Arrigo being hurt when Vergos fell on his leg.
Wellington travel to face Western Sydney next Friday while Victory will host Brisbane next Saturday.
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